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comparison remove.groups.xml @ 1:c32dad34e5ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:24:21 -0400
parents e320a3719431
children 7390f41f4e6b
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0:e320a3719431 1:c32dad34e5ec
2 <description>Remove groups from groups,fasta,names,list,taxonomy</description> 2 <description>Remove groups from groups,fasta,names,list,taxonomy</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 #if $groupnames.source == "other": 13 #if $groupnames.source == "other":
11 ln -s "$groupnames.group_in" groupnames_group_in.dat && 14 ln -s "$groupnames.group_in" groupnames_group_in.dat &&
12 ln -s "$groupnames.fasta_in" groupnames_fasta_in.dat && 15 ln -s "$groupnames.fasta_in" groupnames_fasta_in.dat &&
13 ln -s "$groupnames.name_in" groupnames_name_in.dat && 16 ln -s "$groupnames.name_in" groupnames_name_in.dat &&
41 #end if 44 #end if
42 ,groups=${ str($groupnames.groups).replace(",","-") } 45 ,groups=${ str($groupnames.groups).replace(",","-") }
43 )' 46 )'
44 | sed 's/ //g' ## mothur trips over whitespace 47 | sed 's/ //g' ## mothur trips over whitespace
45 | mothur 48 | mothur
49 | tee mothur.out.log
46 ]]></command> 50 ]]></command>
47 <inputs> 51 <inputs>
48 <conditional name="groupnames"> 52 <conditional name="groupnames">
49 <param name="source" type="select" label="Select Input Type"> 53 <param name="source" type="select" label="Select Input Type">
50 <option value="shared">shared file</option> 54 <option value="shared">shared file</option>
55 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false"> 59 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
56 <options> 60 <options>
57 <filter type="data_meta" ref="group_in" key="groups"/> 61 <filter type="data_meta" ref="group_in" key="groups"/>
58 </options> 62 </options>
59 </param> 63 </param>
60 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> 64 <param name="fasta_in" type="data" format="mothur.align,fasta" optional="true" label="fasta - Fasta Sequences"/>
61 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 65 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
62 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> 66 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
63 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> 67 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
64 </when> 68 </when>
65 <when value="shared"> 69 <when value="shared">
73 </conditional> 77 </conditional>
74 </inputs> 78 </inputs>
75 <outputs> 79 <outputs>
76 <expand macro="logfile-output"/> 80 <expand macro="logfile-output"/>
77 <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> 81 <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
78 <filter>groupname['source'] == 'other' and fasta_in</filter> 82 <filter>groupnames['source'] == 'other' and groupnames['fasta_in']</filter>
79 </data> 83 </data>
80 <data name="group_out" format="mothur.groups" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"> 84 <data name="group_out" format="mothur.groups" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
81 <filter>groupname['source'] == 'other' and group_in</filter> 85 <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.groups'</filter>
86 </data>
87 <data name="count_out" format="mothur.count_table" from_work_dir="groupnames_group_in*.pick.*" label="${tool.name} on ${on_string}: pick.count_table">
88 <filter>groupnames['source'] == 'other' and groupnames['group_in'].ext == 'mothur.count_table'</filter>
82 </data> 89 </data>
83 <data name="name_out" format="mothur.names" from_work_dir="groupnames_name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names"> 90 <data name="name_out" format="mothur.names" from_work_dir="groupnames_name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
84 <filter>groupname['source'] == 'other' and name_in</filter> 91 <filter>groupnames['source'] == 'other' and groupnames['name_in']</filter>
85 </data> 92 </data>
86 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="groupnames_taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy"> 93 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="groupnames_taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
87 <filter>groupname['source'] == 'other' and taxonomy_in</filter> 94 <filter>groupnames['source'] == 'other' and groupnames['taxonomy_in']</filter>
88 </data> 95 </data>
89 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list"> 96 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
90 <filter>groupname['source'] == 'other' and list_in</filter> 97 <filter>groupnames['source'] == 'other' and groupnames['list_in']</filter>
91 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/> 98 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
92 </collection> 99 </collection>
93 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared"> 100 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared">
94 <filter>groupname['source'] == 'shared'</filter> 101 <filter>groupnames['source'] == 'shared'</filter>
95 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/> 102 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
96 </collection> 103 </collection>
97 </outputs> 104 </outputs>
98 <tests> 105 <tests>
99 <test><!-- test with shared file --> 106 <test><!-- test with shared file -->
125 </tests> 132 </tests>
126 <help><![CDATA[ 133 <help><![CDATA[
127 134
128 @MOTHUR_OVERVIEW@ 135 @MOTHUR_OVERVIEW@
129 136
130 **Command Documenation** 137 **Command Documentation**
131 138
132 The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name_, group_, list_, taxonomy_. 139 The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name_, group_, list_, taxonomy_.
133 140
134 .. _name: http://www.mothur.org/wiki/Name_file 141 .. _name: https://www.mothur.org/wiki/Name_file
135 .. _group: http://www.mothur.org/wiki/Group_file 142 .. _group: https://www.mothur.org/wiki/Group_file
136 .. _list: http://www.mothur.org/wiki/List_file 143 .. _list: https://www.mothur.org/wiki/List_file
137 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline 144 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
138 .. _remove.groups: http://www.mothur.org/wiki/Remove.groups 145 .. _remove.groups: https://www.mothur.org/wiki/Remove.groups
139 146
140 ]]> 147 ]]>
141 </help> 148 </help>
142 <expand macro="citations"/> 149 <expand macro="citations"/>
143 </tool> 150 </tool>